Man pages for scristia/CNPBayes
Bayesian mixture models for copy number polymorphisms
| bafLikelihood | Calculate the likelihood of the observed B allele frequencies... |
| batch-method | Retrieve batches from object. |
| bayesFactor | Compute the Bayes factor |
| bic-method | Calculate BIC of a model |
| burnin-method | Number of burnin iterations. |
| chains-method | Retrieve simulated chains from model object. |
| CNPBayes | Bayesian mixture models for copy number estimation |
| cnv_models | Fit a series of Gaussian finite mixture models at a CNV... |
| consensusCNP | Identify consensus start and stop coordinates of a copy... |
| down_sample2 | Downsamples the data to reduce computation |
| findSurrogates-MultiBatch-method | Estimate batch from any sample-level surrogate variables that... |
| fit_restricted2 | Wrapper for running many independent chains with a short... |
| genotype_model | Map mixture component labels to integer copy numbers |
| ggplot-functions | Plotting posterior predictive densities from mixture model |
| hemdel_model | Fits a series of models consistent for a deletion CNV where... |
| homdeldup_model | Wrapper for evaluating mixture models consistent with copy... |
| homdel_model | Wrapper for evaluating mixture models consistent with copy... |
| Hyperparameters | Create an object of class 'Hyperparameters' |
| Hyperparameters-class | An object to specify the hyperparameters of a model. |
| HyperparametersMultiBatch | Create an object of class 'HyperparametersMultiBatch' for the... |
| HyperparametersMultiBatch-class | An object to specify the hyperparameters of a batch effect... |
| HyperparametersSingleBatch | Create an object of class 'HyperparametersSingleBatch' for... |
| HyperparametersSingleBatch-class | An object to specify the hyperparameters of a marginal model. |
| HyperparametersTrios-class | An object to specify the hyperparameters of a model with... |
| hyperParams-method | Accessor for Hyperparameters object for a... |
| id-method | Accessor for sample id |
| isSimulated | Accessor for which observations were simulated |
| iter-method | Reset number of iterations. |
| k-method | Number of components. |
| kolmogorov_batches | Group provisional batch labels by similarity of eCDFs |
| log_lik-method | Retrieve log likelihood. |
| mapping | Map mixture components to copy number states |
| map_z | Calculate the maximum a posteriori estimate of latent... |
| marginal_lik | Accessor for the log marginal likelihood of a SB, SBP, MB, or... |
| marginalLik | Extract marginal likelihoods from a list of models |
| marginalLikelihood-method | Compute the marginal likelihood of a converged model. |
| McmcChains-class | An object to hold estimated paraeters. |
| McmcParams | Create an object of class 'McmcParams' to specify iterations,... |
| McmcParams-class | An object to specify MCMC options for a later simulation |
| mcmcParams-method | Retrieve MCMC parameters from model. |
| mcmcWithHomDel | Wrapper for fitting likely homozygous deletion polymorphisms |
| median_summary | Compute median summaries of log ratios at a CNV region |
| mixture_layout | Layout of grid-based graphics for visualization of posterior... |
| MixtureModel-class | An object for running MCMC simulations. |
| mixture_plot | List of figures useful for evaluating model fit. |
| modelName | Accessor for name of MultiBatch model |
| modelName-MixtureModel-method | Abbreviated model name |
| MultiBatch | Constructor for MultiBatch objects MultiBatch is the... |
| MultiBatch-accessors | MultiBatch accessors |
| MultiBatch-class | An object for running MCMC simulations. |
| MultiBatchList | Constructor for a list of MultiBatch objects |
| MultiBatchModel-class | An object for running MCMC simulations. |
| MultiBatchModelExample | This data is an instance of MultiBatchModel |
| MultiBatchPooledExample | This data is an instance of MultiBatchPooled |
| mu-method | Accessor for mu slot of McmcChains class |
| names-methods | Retrieve the names of the parameters estimated in the MCMC... |
| nStarts-method | Number of random starts for MCMC |
| nu.0-method | Accessor for nu.0 slot of McmcChains class |
| numberObs-method | Number of observations in mixture model object |
| oned-method | Retrieve one-dimensional summaries of the log ratios for each... |
| orderModels | Order models by Bayes factor |
| posteriorSimulation-method | Run MCMC simulation. |
| probz-method | Retrieve the probability of latent variable membership by... |
| revertToMultiBatch | Convert a single-batch object to a multi-batch model |
| sigma2.0-method | Accessor for sigma2.0 slot of McmcChains class |
| sigma2-method | Retrieve the variances of each component and batch... |
| simulateBatchData | Create simulated batch data for testing. |
| simulateData | Create simulated data for testing. |
| SingleBatchCopyNumber-class | Mixture model container where mixture components have been... |
| SingleBatchModel-class | The 'SingleBatchModel' class |
| SingleBatchModelExample | This data is an instance of SingleBatchModel |
| subsetting-methods | Subsetting methods for CNPBayes objects |
| summarize_region | Wrapper for summarizing CNV regions |
| tau2-method | Accessor for tau2 slot of McmcChains class |
| theta-method | Accessor for the theta parameter in the hierarchical mixture... |
| thin-method | Get or set the number of thinning intervals. |
| upsample2 | Provides probabilistic assignments for mixture components to... |
| warmup | Run short burnin from multiple independent starts and select... |
| zfreq-method | Accessor for frequency of mixture component label in... |
| z-method | Retrieve latent variable assignments. |
